Discordance is telling us something about "species"

Brent Mishler

Discordance has always been a problem with species concepts, a problem that has become
increasingly acute given modern genomic data. Ecological criteria often do not pick
out the same entities as breeding criteria. Phylogenetic criteria often do not pick
out the same entities as either ecological criteria or breeding criteria. Phylogenies
of different genes often pick out different entities. This obvious discordance has
prompted some (including the present author in an earlier incarnation) to advocate
pluralistic species concepts.

What we were all missing is something only Darwin has seen clearly: there is no real
species level. Divergence happens, driven by various factors external and internal
to the organism. At some point we might call something a species for the sake of convenience,
but nothing magical has happened at that point. Lineages (a diachronic connection
between ancestor and descendant) and clades (a synchronic set of relatives forming
a monophyletic group) are real, but not any particular taxonomic rank, including species.

Likewise, the traditional cladistic concept of monophyly has become problematic given
the discordance revealed by modern genomic data. Given problems of lineage sorting,
and horizontal transfer that may happen at any depth in the tree of life, we can no
longer require monophyly of a set of organisms to be supported by all genes in the
genome (the co-called exclusivity criterion). There are no monophyletic groups, at
any level, using such a strict definition. Instead, monophyly needs to be viewed as
an ensemble characteristic of descent in a set of organisms -- a monophyletic group
is one supported by a majority of gene phylogenies, with incongruent gene phylogenies
needing a separate explanation.

Discordance is telling us that we need to get rid of the species rank entirely and
concentrate on finding, naming, and studying monophyletic groups at all levels using
a rankless classification system like a suitably modified PhyloCode. The species rank
is a long-outdated remnant of pre-Darwinian, creationistic biology. It turns out that
the reason it has been impossible over the last century to define the species rank
coherently is because it corresponds to nothing real. It's time for biologists to
move on, and finally catch up with Darwin!